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Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

Josiemer Mattei12, Laurence D Parnell1, Chao-Qiang Lai1, Bibiana Garcia-Bailo3, Xian Adiconis4, Jian Shen1, Donna Arnett5, Serkalem Demissie6, Katherine L Tucker12 and Jose M Ordovas12*

Author Affiliations

1 Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA

2 Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA

3 Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada

4 Genome Biology and Cell Circuits Program, Broad Institute, Cambridge, MA, USA

5 Department of Epidemiology, University of Alabama, Birmingham, Birmingham, AL, USA

6 Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA

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BMC Genetics 2009, 10:45  doi:10.1186/1471-2156-10-45

Published: 14 August 2009



Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs) in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years) and compared them to similarly aged non-Hispanic whites (NHW) (n = 597).


Minor allele frequency (MAF) distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only.


These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans.